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. 2021 Jun 16;11:12728. doi: 10.1038/s41598-021-91456-0

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021

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Overview of AMRFinderPlus gene identification method using protein and nucleotide sequences. When AMRFinderPlus is run in protein-only or nucleotide-only modes only the relevant side of the flowchart above is utilized. Note that HMMs are not used with nucleotide-only data which results in reduced sensitivity for some families. "Ignored" matches are not used, however an alternative method may still report the protein (e.g., an ignored HMM match will not suppress reporting based on BLASTP or BLASTX hit). *Details are simplified in this diagram; a more detailed description is included in the methods text.